Multiple sequence alignment - TraesCS7D01G130200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G130200 chr7D 100.000 4487 0 0 1 4487 82450243 82445757 0.000000e+00 8287.0
1 TraesCS7D01G130200 chr7D 77.732 1446 213 59 2251 3640 73611741 73610349 0.000000e+00 785.0
2 TraesCS7D01G130200 chr7D 80.280 644 93 21 3000 3640 73563547 73562935 5.290000e-124 455.0
3 TraesCS7D01G130200 chr7D 77.400 677 107 24 1755 2397 82348553 82347889 1.190000e-95 361.0
4 TraesCS7D01G130200 chr7D 84.713 157 19 3 1993 2146 73180287 73180441 7.770000e-33 152.0
5 TraesCS7D01G130200 chr7D 74.704 253 43 14 1167 1408 548818455 548818213 4.780000e-15 93.5
6 TraesCS7D01G130200 chr7B 93.381 3520 171 31 384 3869 29830578 29827087 0.000000e+00 5153.0
7 TraesCS7D01G130200 chr7B 93.827 2754 113 23 1757 4481 30765400 30762675 0.000000e+00 4091.0
8 TraesCS7D01G130200 chr7B 93.673 2434 108 20 334 2735 31448785 31446366 0.000000e+00 3600.0
9 TraesCS7D01G130200 chr7B 92.716 2169 95 28 2223 4353 31442850 31440707 0.000000e+00 3072.0
10 TraesCS7D01G130200 chr7B 95.127 1067 47 2 668 1732 30766457 30765394 0.000000e+00 1677.0
11 TraesCS7D01G130200 chr7B 89.458 977 61 14 2117 3082 31444966 31444021 0.000000e+00 1195.0
12 TraesCS7D01G130200 chr7B 95.359 711 21 5 2751 3458 31446379 31445678 0.000000e+00 1120.0
13 TraesCS7D01G130200 chr7B 95.534 627 15 4 3867 4482 29827005 29826381 0.000000e+00 990.0
14 TraesCS7D01G130200 chr7B 91.564 652 28 8 1223 1872 31445681 31445055 0.000000e+00 874.0
15 TraesCS7D01G130200 chr7B 81.806 731 111 16 2924 3640 16828080 16828802 1.070000e-165 593.0
16 TraesCS7D01G130200 chr7B 83.109 521 84 4 3123 3640 16734044 16734563 5.250000e-129 472.0
17 TraesCS7D01G130200 chr7B 90.823 316 24 4 2315 2628 31444025 31443713 6.940000e-113 418.0
18 TraesCS7D01G130200 chr7B 79.242 607 90 22 940 1538 29608558 29607980 1.510000e-104 390.0
19 TraesCS7D01G130200 chr7B 77.778 531 75 21 1755 2250 29607933 29607411 2.040000e-73 287.0
20 TraesCS7D01G130200 chr7B 90.576 191 7 4 334 524 30770018 30769839 4.480000e-60 243.0
21 TraesCS7D01G130200 chr7B 79.233 313 39 19 2467 2763 732855095 732855397 1.270000e-45 195.0
22 TraesCS7D01G130200 chr7B 93.388 121 6 2 213 333 31448953 31448835 1.280000e-40 178.0
23 TraesCS7D01G130200 chr7B 91.736 121 6 4 213 333 30770184 30770068 9.990000e-37 165.0
24 TraesCS7D01G130200 chr7B 77.852 298 40 14 1866 2146 15936119 15936407 1.290000e-35 161.0
25 TraesCS7D01G130200 chr7B 86.957 92 9 2 3940 4028 30763151 30763060 2.860000e-17 100.0
26 TraesCS7D01G130200 chr7B 78.014 141 21 4 3927 4057 674189864 674190004 3.720000e-11 80.5
27 TraesCS7D01G130200 chr7A 93.365 2984 106 23 348 3263 84248825 84245866 0.000000e+00 4329.0
28 TraesCS7D01G130200 chr7A 94.054 1194 35 9 3297 4487 84245870 84244710 0.000000e+00 1779.0
29 TraesCS7D01G130200 chr7A 82.167 443 62 7 3203 3640 78133328 78132898 9.170000e-97 364.0
30 TraesCS7D01G130200 chr7A 77.061 667 99 34 1755 2397 84026351 84025715 7.190000e-88 335.0
31 TraesCS7D01G130200 chr7A 75.142 881 123 37 688 1537 78387965 78388780 4.330000e-85 326.0
32 TraesCS7D01G130200 chr7A 81.886 403 39 14 3261 3642 84025712 84025323 4.360000e-80 309.0
33 TraesCS7D01G130200 chr1B 84.325 504 67 9 2924 3423 15262878 15262383 2.430000e-132 483.0
34 TraesCS7D01G130200 chr1B 76.136 176 29 11 4 175 548832351 548832517 3.720000e-11 80.5
35 TraesCS7D01G130200 chr2B 79.343 731 94 33 2492 3195 601733596 601734296 1.140000e-125 460.0
36 TraesCS7D01G130200 chr2B 79.613 569 85 21 848 1407 55210336 55209790 3.280000e-101 379.0
37 TraesCS7D01G130200 chr2B 78.857 525 63 27 3136 3646 55854305 55853815 1.210000e-80 311.0
38 TraesCS7D01G130200 chr2B 100.000 28 0 0 1510 1537 54887355 54887328 8.000000e-03 52.8
39 TraesCS7D01G130200 chr6A 78.331 743 104 32 2492 3206 561602197 561601484 1.150000e-115 427.0
40 TraesCS7D01G130200 chr2A 78.819 576 97 19 848 1413 36400207 36399647 9.170000e-97 364.0
41 TraesCS7D01G130200 chr2A 78.819 576 94 21 848 1413 36411856 36411299 3.300000e-96 363.0
42 TraesCS7D01G130200 chr2A 83.832 167 23 4 1998 2161 36410904 36410739 6.010000e-34 156.0
43 TraesCS7D01G130200 chr2A 100.000 28 0 0 1510 1537 36202236 36202209 8.000000e-03 52.8
44 TraesCS7D01G130200 chr2D 78.415 593 86 25 824 1407 33581180 33580621 9.240000e-92 348.0
45 TraesCS7D01G130200 chr2D 77.220 518 75 24 3136 3642 33372555 33372070 3.440000e-66 263.0
46 TraesCS7D01G130200 chr2D 78.667 300 40 17 1867 2151 33164257 33163967 1.280000e-40 178.0
47 TraesCS7D01G130200 chr2D 84.314 153 22 2 2001 2152 79086243 79086394 1.010000e-31 148.0
48 TraesCS7D01G130200 chr6B 78.846 312 42 17 2467 2763 710256995 710256693 5.930000e-44 189.0
49 TraesCS7D01G130200 chr6B 78.594 313 41 20 2467 2763 466652910 466653212 2.760000e-42 183.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G130200 chr7D 82445757 82450243 4486 True 8287.000000 8287 100.000000 1 4487 1 chr7D.!!$R4 4486
1 TraesCS7D01G130200 chr7D 73610349 73611741 1392 True 785.000000 785 77.732000 2251 3640 1 chr7D.!!$R2 1389
2 TraesCS7D01G130200 chr7D 73562935 73563547 612 True 455.000000 455 80.280000 3000 3640 1 chr7D.!!$R1 640
3 TraesCS7D01G130200 chr7D 82347889 82348553 664 True 361.000000 361 77.400000 1755 2397 1 chr7D.!!$R3 642
4 TraesCS7D01G130200 chr7B 29826381 29830578 4197 True 3071.500000 5153 94.457500 384 4482 2 chr7B.!!$R2 4098
5 TraesCS7D01G130200 chr7B 31440707 31448953 8246 True 1493.857143 3600 92.425857 213 4353 7 chr7B.!!$R4 4140
6 TraesCS7D01G130200 chr7B 30762675 30770184 7509 True 1255.200000 4091 91.644600 213 4481 5 chr7B.!!$R3 4268
7 TraesCS7D01G130200 chr7B 16828080 16828802 722 False 593.000000 593 81.806000 2924 3640 1 chr7B.!!$F3 716
8 TraesCS7D01G130200 chr7B 16734044 16734563 519 False 472.000000 472 83.109000 3123 3640 1 chr7B.!!$F2 517
9 TraesCS7D01G130200 chr7B 29607411 29608558 1147 True 338.500000 390 78.510000 940 2250 2 chr7B.!!$R1 1310
10 TraesCS7D01G130200 chr7A 84244710 84248825 4115 True 3054.000000 4329 93.709500 348 4487 2 chr7A.!!$R3 4139
11 TraesCS7D01G130200 chr7A 78387965 78388780 815 False 326.000000 326 75.142000 688 1537 1 chr7A.!!$F1 849
12 TraesCS7D01G130200 chr7A 84025323 84026351 1028 True 322.000000 335 79.473500 1755 3642 2 chr7A.!!$R2 1887
13 TraesCS7D01G130200 chr2B 601733596 601734296 700 False 460.000000 460 79.343000 2492 3195 1 chr2B.!!$F1 703
14 TraesCS7D01G130200 chr2B 55209790 55210336 546 True 379.000000 379 79.613000 848 1407 1 chr2B.!!$R2 559
15 TraesCS7D01G130200 chr6A 561601484 561602197 713 True 427.000000 427 78.331000 2492 3206 1 chr6A.!!$R1 714
16 TraesCS7D01G130200 chr2A 36399647 36400207 560 True 364.000000 364 78.819000 848 1413 1 chr2A.!!$R2 565
17 TraesCS7D01G130200 chr2A 36410739 36411856 1117 True 259.500000 363 81.325500 848 2161 2 chr2A.!!$R3 1313
18 TraesCS7D01G130200 chr2D 33580621 33581180 559 True 348.000000 348 78.415000 824 1407 1 chr2D.!!$R3 583

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
206 207 0.099968 TAGCCAGATCCGACGTTTCG 59.900 55.0 0.00 0.0 45.44 3.46 F
1153 4488 0.035056 GGTGCACATCTACCAAGGCT 60.035 55.0 20.43 0.0 36.94 4.58 F
1733 5136 0.042967 GTCGAAATTCCTGATCGCGC 60.043 55.0 0.00 0.0 36.56 6.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1854 5285 1.227263 CGAACCGAATCTCCCGCAT 60.227 57.895 0.0 0.0 0.0 4.73 R
2841 6357 1.901591 ATTGAAGACCACCAGTGCAG 58.098 50.000 0.0 0.0 0.0 4.41 R
3607 11312 1.871080 AGAAACACAAGAGCTGACGG 58.129 50.000 0.0 0.0 0.0 4.79 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 4.376340 AAAAACTGCAACAAGACCTCAG 57.624 40.909 0.00 0.00 0.00 3.35
31 32 2.717639 AACTGCAACAAGACCTCAGT 57.282 45.000 0.00 0.00 39.42 3.41
32 33 2.717639 ACTGCAACAAGACCTCAGTT 57.282 45.000 0.00 0.00 34.69 3.16
33 34 2.292267 ACTGCAACAAGACCTCAGTTG 58.708 47.619 0.00 0.00 44.01 3.16
37 38 3.781079 CAACAAGACCTCAGTTGCAAA 57.219 42.857 0.00 0.00 36.59 3.68
38 39 3.699067 CAACAAGACCTCAGTTGCAAAG 58.301 45.455 0.00 0.00 36.59 2.77
39 40 3.281727 ACAAGACCTCAGTTGCAAAGA 57.718 42.857 0.00 1.16 0.00 2.52
40 41 3.620488 ACAAGACCTCAGTTGCAAAGAA 58.380 40.909 0.00 0.00 0.00 2.52
41 42 4.016444 ACAAGACCTCAGTTGCAAAGAAA 58.984 39.130 0.00 0.00 0.00 2.52
42 43 4.142381 ACAAGACCTCAGTTGCAAAGAAAC 60.142 41.667 0.00 0.00 0.00 2.78
43 44 3.891049 AGACCTCAGTTGCAAAGAAACT 58.109 40.909 0.00 0.00 38.40 2.66
52 53 3.865011 TGCAAAGAAACTGCAACAAGA 57.135 38.095 0.00 0.00 46.47 3.02
53 54 4.389890 TGCAAAGAAACTGCAACAAGAT 57.610 36.364 0.00 0.00 46.47 2.40
54 55 4.362279 TGCAAAGAAACTGCAACAAGATC 58.638 39.130 0.00 0.00 46.47 2.75
55 56 4.098349 TGCAAAGAAACTGCAACAAGATCT 59.902 37.500 0.00 0.00 46.47 2.75
56 57 4.678742 GCAAAGAAACTGCAACAAGATCTC 59.321 41.667 0.00 0.00 39.69 2.75
57 58 5.734220 GCAAAGAAACTGCAACAAGATCTCA 60.734 40.000 0.00 0.00 39.69 3.27
58 59 5.686159 AAGAAACTGCAACAAGATCTCAG 57.314 39.130 0.00 0.83 0.00 3.35
59 60 4.712476 AGAAACTGCAACAAGATCTCAGT 58.288 39.130 7.93 7.93 39.42 3.41
60 61 5.128919 AGAAACTGCAACAAGATCTCAGTT 58.871 37.500 16.88 16.88 46.27 3.16
61 62 4.825546 AACTGCAACAAGATCTCAGTTG 57.174 40.909 25.37 25.37 43.72 3.16
70 71 8.752766 CAACAAGATCTCAGTTGCAAATTATT 57.247 30.769 21.08 0.00 36.59 1.40
71 72 9.199982 CAACAAGATCTCAGTTGCAAATTATTT 57.800 29.630 21.08 0.00 36.59 1.40
72 73 9.768662 AACAAGATCTCAGTTGCAAATTATTTT 57.231 25.926 0.00 0.00 0.00 1.82
73 74 9.768662 ACAAGATCTCAGTTGCAAATTATTTTT 57.231 25.926 0.00 0.00 0.00 1.94
111 112 5.514059 TTTTTGCGAAATAATTCTGCAGC 57.486 34.783 9.47 0.00 42.00 5.25
112 113 3.846423 TTGCGAAATAATTCTGCAGCA 57.154 38.095 9.47 0.00 42.00 4.41
113 114 4.374843 TTGCGAAATAATTCTGCAGCAT 57.625 36.364 9.47 0.00 42.00 3.79
114 115 3.697982 TGCGAAATAATTCTGCAGCATG 58.302 40.909 9.47 0.00 38.89 4.06
115 116 3.377798 TGCGAAATAATTCTGCAGCATGA 59.622 39.130 9.47 0.00 38.89 3.07
116 117 3.727723 GCGAAATAATTCTGCAGCATGAC 59.272 43.478 9.47 0.00 36.09 3.06
117 118 4.285292 CGAAATAATTCTGCAGCATGACC 58.715 43.478 9.47 0.00 33.19 4.02
118 119 3.976793 AATAATTCTGCAGCATGACCG 57.023 42.857 9.47 0.00 39.69 4.79
119 120 1.667236 TAATTCTGCAGCATGACCGG 58.333 50.000 9.47 0.00 39.69 5.28
120 121 1.033746 AATTCTGCAGCATGACCGGG 61.034 55.000 9.47 0.00 39.69 5.73
121 122 2.202236 ATTCTGCAGCATGACCGGGT 62.202 55.000 9.47 0.00 39.69 5.28
122 123 2.360350 CTGCAGCATGACCGGGTT 60.360 61.111 6.32 0.00 39.69 4.11
123 124 1.973281 CTGCAGCATGACCGGGTTT 60.973 57.895 6.32 0.00 39.69 3.27
124 125 2.203972 CTGCAGCATGACCGGGTTTG 62.204 60.000 6.32 3.83 39.69 2.93
125 126 2.268076 GCAGCATGACCGGGTTTGT 61.268 57.895 6.32 0.00 39.69 2.83
126 127 0.958382 GCAGCATGACCGGGTTTGTA 60.958 55.000 6.32 0.00 39.69 2.41
127 128 1.086696 CAGCATGACCGGGTTTGTAG 58.913 55.000 6.32 0.00 39.69 2.74
128 129 0.981183 AGCATGACCGGGTTTGTAGA 59.019 50.000 6.32 0.00 0.00 2.59
129 130 1.349688 AGCATGACCGGGTTTGTAGAA 59.650 47.619 6.32 0.00 0.00 2.10
130 131 2.156098 GCATGACCGGGTTTGTAGAAA 58.844 47.619 6.32 0.00 0.00 2.52
131 132 2.554893 GCATGACCGGGTTTGTAGAAAA 59.445 45.455 6.32 0.00 0.00 2.29
132 133 3.192633 GCATGACCGGGTTTGTAGAAAAT 59.807 43.478 6.32 0.00 0.00 1.82
133 134 4.321675 GCATGACCGGGTTTGTAGAAAATT 60.322 41.667 6.32 0.00 0.00 1.82
134 135 5.106078 GCATGACCGGGTTTGTAGAAAATTA 60.106 40.000 6.32 0.00 0.00 1.40
135 136 5.945466 TGACCGGGTTTGTAGAAAATTAC 57.055 39.130 6.32 0.00 0.00 1.89
136 137 4.761227 TGACCGGGTTTGTAGAAAATTACC 59.239 41.667 6.32 0.00 0.00 2.85
137 138 3.752747 ACCGGGTTTGTAGAAAATTACCG 59.247 43.478 6.32 10.23 38.59 4.02
138 139 3.426560 CCGGGTTTGTAGAAAATTACCGC 60.427 47.826 11.20 0.00 37.63 5.68
139 140 3.188873 CGGGTTTGTAGAAAATTACCGCA 59.811 43.478 6.24 0.00 31.93 5.69
140 141 4.320348 CGGGTTTGTAGAAAATTACCGCAA 60.320 41.667 6.24 0.00 31.93 4.85
141 142 4.919168 GGGTTTGTAGAAAATTACCGCAAC 59.081 41.667 0.00 0.00 0.00 4.17
142 143 5.507650 GGGTTTGTAGAAAATTACCGCAACA 60.508 40.000 0.00 0.00 0.00 3.33
143 144 5.400188 GGTTTGTAGAAAATTACCGCAACAC 59.600 40.000 0.00 0.00 0.00 3.32
144 145 5.752892 TTGTAGAAAATTACCGCAACACA 57.247 34.783 0.00 0.00 0.00 3.72
145 146 5.752892 TGTAGAAAATTACCGCAACACAA 57.247 34.783 0.00 0.00 0.00 3.33
146 147 5.512473 TGTAGAAAATTACCGCAACACAAC 58.488 37.500 0.00 0.00 0.00 3.32
147 148 3.972403 AGAAAATTACCGCAACACAACC 58.028 40.909 0.00 0.00 0.00 3.77
148 149 3.634910 AGAAAATTACCGCAACACAACCT 59.365 39.130 0.00 0.00 0.00 3.50
149 150 4.098807 AGAAAATTACCGCAACACAACCTT 59.901 37.500 0.00 0.00 0.00 3.50
150 151 4.394439 AAATTACCGCAACACAACCTTT 57.606 36.364 0.00 0.00 0.00 3.11
151 152 2.853731 TTACCGCAACACAACCTTTG 57.146 45.000 0.00 0.00 0.00 2.77
152 153 1.752683 TACCGCAACACAACCTTTGT 58.247 45.000 0.00 0.00 46.75 2.83
153 154 0.892063 ACCGCAACACAACCTTTGTT 59.108 45.000 0.00 0.00 43.23 2.83
167 168 6.222389 CAACCTTTGTTGCAATGATAAAGGA 58.778 36.000 31.72 0.00 46.43 3.36
168 169 6.610075 ACCTTTGTTGCAATGATAAAGGAT 57.390 33.333 31.72 21.55 46.43 3.24
169 170 6.400568 ACCTTTGTTGCAATGATAAAGGATG 58.599 36.000 31.72 18.22 46.43 3.51
170 171 6.211184 ACCTTTGTTGCAATGATAAAGGATGA 59.789 34.615 31.72 0.00 46.43 2.92
171 172 6.532657 CCTTTGTTGCAATGATAAAGGATGAC 59.467 38.462 26.49 5.39 46.43 3.06
172 173 5.233957 TGTTGCAATGATAAAGGATGACG 57.766 39.130 0.59 0.00 0.00 4.35
173 174 3.969117 TGCAATGATAAAGGATGACGC 57.031 42.857 0.00 0.00 0.00 5.19
174 175 3.544684 TGCAATGATAAAGGATGACGCT 58.455 40.909 0.00 0.00 0.00 5.07
175 176 3.947196 TGCAATGATAAAGGATGACGCTT 59.053 39.130 0.00 0.00 0.00 4.68
176 177 5.122519 TGCAATGATAAAGGATGACGCTTA 58.877 37.500 0.00 0.00 0.00 3.09
177 178 5.588246 TGCAATGATAAAGGATGACGCTTAA 59.412 36.000 0.00 0.00 0.00 1.85
178 179 6.138761 GCAATGATAAAGGATGACGCTTAAG 58.861 40.000 0.00 0.00 0.00 1.85
179 180 5.931441 ATGATAAAGGATGACGCTTAAGC 57.069 39.130 17.83 17.83 37.78 3.09
198 199 1.365633 GCTCACCTAGCCAGATCCG 59.634 63.158 0.00 0.00 46.25 4.18
199 200 1.109920 GCTCACCTAGCCAGATCCGA 61.110 60.000 0.00 0.00 46.25 4.55
200 201 0.671251 CTCACCTAGCCAGATCCGAC 59.329 60.000 0.00 0.00 0.00 4.79
201 202 1.101635 TCACCTAGCCAGATCCGACG 61.102 60.000 0.00 0.00 0.00 5.12
202 203 1.076923 ACCTAGCCAGATCCGACGT 60.077 57.895 0.00 0.00 0.00 4.34
203 204 0.683504 ACCTAGCCAGATCCGACGTT 60.684 55.000 0.00 0.00 0.00 3.99
204 205 0.460311 CCTAGCCAGATCCGACGTTT 59.540 55.000 0.00 0.00 0.00 3.60
205 206 1.536284 CCTAGCCAGATCCGACGTTTC 60.536 57.143 0.00 0.00 0.00 2.78
206 207 0.099968 TAGCCAGATCCGACGTTTCG 59.900 55.000 0.00 0.00 45.44 3.46
207 208 2.799540 GCCAGATCCGACGTTTCGC 61.800 63.158 0.00 0.00 44.43 4.70
208 209 2.505498 CCAGATCCGACGTTTCGCG 61.505 63.158 0.00 0.00 44.43 5.87
209 210 1.513373 CAGATCCGACGTTTCGCGA 60.513 57.895 3.71 3.71 44.43 5.87
210 211 1.226323 AGATCCGACGTTTCGCGAG 60.226 57.895 9.59 0.00 44.43 5.03
211 212 2.202570 ATCCGACGTTTCGCGAGG 60.203 61.111 9.59 6.15 44.43 4.63
230 231 5.932303 GCGAGGCCATAAATGAATTAGAGTA 59.068 40.000 5.01 0.00 0.00 2.59
251 252 5.594317 AGTATGAACTTGGGATTTACATGCC 59.406 40.000 0.00 0.00 41.41 4.40
324 325 7.535258 CCGAAACTTCATAACAGAGTTTTCATG 59.465 37.037 2.68 0.00 33.53 3.07
325 326 8.070171 CGAAACTTCATAACAGAGTTTTCATGT 58.930 33.333 2.68 0.00 33.53 3.21
331 332 8.006298 TCATAACAGAGTTTTCATGTGGTTTT 57.994 30.769 0.00 0.00 0.00 2.43
332 333 8.134895 TCATAACAGAGTTTTCATGTGGTTTTC 58.865 33.333 0.00 0.00 0.00 2.29
343 392 4.092821 TCATGTGGTTTTCATCGATTCGAC 59.907 41.667 11.56 0.00 39.18 4.20
368 417 2.816087 CAATGACAGCAAAGCAGGTAGT 59.184 45.455 0.00 0.00 0.00 2.73
369 418 3.981071 ATGACAGCAAAGCAGGTAGTA 57.019 42.857 0.00 0.00 0.00 1.82
370 419 3.319137 TGACAGCAAAGCAGGTAGTAG 57.681 47.619 0.00 0.00 0.00 2.57
371 420 2.028112 TGACAGCAAAGCAGGTAGTAGG 60.028 50.000 0.00 0.00 0.00 3.18
458 519 0.251354 GGCAGTTCTGCTGGATCTGA 59.749 55.000 21.46 0.00 45.14 3.27
475 536 1.219124 GATGGTGCTTCGCTCCTCA 59.781 57.895 8.22 0.00 42.02 3.86
686 3988 3.775654 AAGCTCGCCGGGGAAGAG 61.776 66.667 22.77 12.07 35.28 2.85
860 4176 3.775661 AATTTCGCCTTCAAATACCCG 57.224 42.857 0.00 0.00 0.00 5.28
978 4310 3.535962 CTCCTCTGCTCTCCGGCC 61.536 72.222 0.00 0.00 0.00 6.13
1076 4411 4.849329 CTACCTCCACGCCGACGC 62.849 72.222 0.00 0.00 45.53 5.19
1153 4488 0.035056 GGTGCACATCTACCAAGGCT 60.035 55.000 20.43 0.00 36.94 4.58
1567 4944 0.246635 TTGCTTCCGTCTGAGCCTAC 59.753 55.000 0.00 0.00 0.00 3.18
1568 4945 0.612174 TGCTTCCGTCTGAGCCTACT 60.612 55.000 0.00 0.00 0.00 2.57
1569 4946 1.340697 TGCTTCCGTCTGAGCCTACTA 60.341 52.381 0.00 0.00 0.00 1.82
1733 5136 0.042967 GTCGAAATTCCTGATCGCGC 60.043 55.000 0.00 0.00 36.56 6.86
1956 5401 1.359168 GGGGAGGTCCTTGTACAACT 58.641 55.000 3.59 0.00 35.95 3.16
2283 5761 3.517296 TTTGGTGGGCTGTTAATCTGA 57.483 42.857 0.00 0.00 0.00 3.27
2431 5913 6.067263 TGTCGACTTTTTGGTTAATGGAAG 57.933 37.500 17.92 0.00 0.00 3.46
2444 5926 7.818642 TGGTTAATGGAAGGTAACATTTTACG 58.181 34.615 0.00 0.00 38.88 3.18
2447 5929 6.584185 AATGGAAGGTAACATTTTACGCTT 57.416 33.333 5.64 5.64 38.88 4.68
2734 6239 8.860088 TCTAGTTTCTGCACATGAGCTATATTA 58.140 33.333 16.24 2.17 34.99 0.98
2742 6247 7.587629 TGCACATGAGCTATATTATTTTCAGC 58.412 34.615 16.24 0.00 34.99 4.26
2841 6357 9.654663 TTCCTGCTAATCTTCTTTTACTAGAAC 57.345 33.333 0.00 0.00 31.19 3.01
2915 6432 5.356190 AGATCTGTTTACTGCATGAACATGG 59.644 40.000 15.15 3.82 36.31 3.66
2936 6481 5.967088 TGGTATCTGAAGTCTGTCTTTAGC 58.033 41.667 2.41 0.00 38.92 3.09
3076 6631 3.118454 GTGTCGATGCCGTGTGGG 61.118 66.667 0.00 0.00 37.05 4.61
3090 6650 3.448686 CGTGTGGGTCTATCAATCTGTC 58.551 50.000 0.00 0.00 0.00 3.51
3098 6658 6.725834 TGGGTCTATCAATCTGTCTATGCATA 59.274 38.462 6.20 6.20 0.00 3.14
3207 6774 2.604046 AGCATTTAGTCGCCAGTAGG 57.396 50.000 0.00 0.00 38.23 3.18
3381 11060 9.950680 GTTTCATGTTTTGTCTTCTTGATCTTA 57.049 29.630 0.00 0.00 0.00 2.10
3502 11193 2.302260 CGTAGAGAAGGATCAGAGCCA 58.698 52.381 7.64 0.00 0.00 4.75
3609 11314 7.897864 AGATAGATATAGGTTGAGAAAACCCG 58.102 38.462 3.66 0.00 41.18 5.28
3697 11402 6.543465 TCACACTTCTGACATTCATTTCTGTT 59.457 34.615 0.00 0.00 0.00 3.16
3905 11695 5.063691 GTGAGCTGATGATCTTGTTTCTCAG 59.936 44.000 0.00 0.00 34.61 3.35
4122 11934 4.837896 TGTGTTGTGTTGTTTTGAGTGA 57.162 36.364 0.00 0.00 0.00 3.41
4306 12131 3.263170 TGCCTCAGTGTTCCTGCTTAATA 59.737 43.478 0.00 0.00 41.25 0.98
4421 12247 9.274206 ACTTGAGTTTATCTGTTTCTAACTTCC 57.726 33.333 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.763897 ACTGAGGTCTTGTTGCAGTTTTT 59.236 39.130 0.00 0.00 36.49 1.94
10 11 3.356290 ACTGAGGTCTTGTTGCAGTTTT 58.644 40.909 0.00 0.00 36.49 2.43
11 12 3.004752 ACTGAGGTCTTGTTGCAGTTT 57.995 42.857 0.00 0.00 36.49 2.66
12 13 2.717639 ACTGAGGTCTTGTTGCAGTT 57.282 45.000 0.00 0.00 36.49 3.16
13 14 2.292267 CAACTGAGGTCTTGTTGCAGT 58.708 47.619 0.00 0.00 41.19 4.40
17 18 3.378112 TCTTTGCAACTGAGGTCTTGTTG 59.622 43.478 0.00 0.00 42.55 3.33
18 19 3.620488 TCTTTGCAACTGAGGTCTTGTT 58.380 40.909 0.00 0.00 0.00 2.83
19 20 3.281727 TCTTTGCAACTGAGGTCTTGT 57.718 42.857 0.00 0.00 0.00 3.16
20 21 4.096984 AGTTTCTTTGCAACTGAGGTCTTG 59.903 41.667 0.00 0.00 33.04 3.02
21 22 4.273318 AGTTTCTTTGCAACTGAGGTCTT 58.727 39.130 0.00 0.00 33.04 3.01
22 23 3.891049 AGTTTCTTTGCAACTGAGGTCT 58.109 40.909 0.00 0.00 33.04 3.85
33 34 4.614946 AGATCTTGTTGCAGTTTCTTTGC 58.385 39.130 0.00 0.00 41.86 3.68
34 35 5.824429 TGAGATCTTGTTGCAGTTTCTTTG 58.176 37.500 0.00 0.00 0.00 2.77
35 36 5.591877 ACTGAGATCTTGTTGCAGTTTCTTT 59.408 36.000 7.93 0.00 36.49 2.52
36 37 5.128919 ACTGAGATCTTGTTGCAGTTTCTT 58.871 37.500 7.93 0.00 36.49 2.52
37 38 4.712476 ACTGAGATCTTGTTGCAGTTTCT 58.288 39.130 7.93 0.00 36.49 2.52
38 39 5.210715 CAACTGAGATCTTGTTGCAGTTTC 58.789 41.667 19.01 0.00 44.68 2.78
39 40 5.179045 CAACTGAGATCTTGTTGCAGTTT 57.821 39.130 19.01 7.01 44.68 2.66
45 46 8.752766 AATAATTTGCAACTGAGATCTTGTTG 57.247 30.769 25.43 25.43 42.55 3.33
46 47 9.768662 AAAATAATTTGCAACTGAGATCTTGTT 57.231 25.926 0.00 2.90 0.00 2.83
47 48 9.768662 AAAAATAATTTGCAACTGAGATCTTGT 57.231 25.926 0.00 0.00 0.00 3.16
89 90 4.987285 TGCTGCAGAATTATTTCGCAAAAA 59.013 33.333 20.43 0.00 39.27 1.94
90 91 4.554292 TGCTGCAGAATTATTTCGCAAAA 58.446 34.783 20.43 6.46 39.27 2.44
91 92 4.171663 TGCTGCAGAATTATTTCGCAAA 57.828 36.364 20.43 6.68 39.27 3.68
92 93 3.846423 TGCTGCAGAATTATTTCGCAA 57.154 38.095 20.43 3.33 39.27 4.85
93 94 3.377798 TCATGCTGCAGAATTATTTCGCA 59.622 39.130 20.43 4.97 38.29 5.10
94 95 3.727723 GTCATGCTGCAGAATTATTTCGC 59.272 43.478 20.43 0.00 36.93 4.70
95 96 4.285292 GGTCATGCTGCAGAATTATTTCG 58.715 43.478 20.43 0.00 36.93 3.46
96 97 4.285292 CGGTCATGCTGCAGAATTATTTC 58.715 43.478 20.43 0.00 0.00 2.17
97 98 3.067180 CCGGTCATGCTGCAGAATTATTT 59.933 43.478 20.43 0.00 0.00 1.40
98 99 2.620115 CCGGTCATGCTGCAGAATTATT 59.380 45.455 20.43 0.00 0.00 1.40
99 100 2.224606 CCGGTCATGCTGCAGAATTAT 58.775 47.619 20.43 2.48 0.00 1.28
100 101 1.667236 CCGGTCATGCTGCAGAATTA 58.333 50.000 20.43 0.00 0.00 1.40
101 102 1.033746 CCCGGTCATGCTGCAGAATT 61.034 55.000 20.43 0.00 0.00 2.17
102 103 1.452651 CCCGGTCATGCTGCAGAAT 60.453 57.895 20.43 10.50 0.00 2.40
103 104 2.046023 CCCGGTCATGCTGCAGAA 60.046 61.111 20.43 7.68 0.00 3.02
104 105 2.410322 AAACCCGGTCATGCTGCAGA 62.410 55.000 20.43 2.70 0.00 4.26
105 106 1.973281 AAACCCGGTCATGCTGCAG 60.973 57.895 10.11 10.11 0.00 4.41
106 107 2.115052 AAACCCGGTCATGCTGCA 59.885 55.556 4.13 4.13 0.00 4.41
107 108 0.958382 TACAAACCCGGTCATGCTGC 60.958 55.000 0.00 0.00 0.00 5.25
108 109 1.086696 CTACAAACCCGGTCATGCTG 58.913 55.000 0.00 0.00 0.00 4.41
109 110 0.981183 TCTACAAACCCGGTCATGCT 59.019 50.000 0.00 0.00 0.00 3.79
110 111 1.816074 TTCTACAAACCCGGTCATGC 58.184 50.000 0.00 0.00 0.00 4.06
111 112 5.385509 AATTTTCTACAAACCCGGTCATG 57.614 39.130 0.00 0.00 0.00 3.07
112 113 5.416639 GGTAATTTTCTACAAACCCGGTCAT 59.583 40.000 0.00 0.00 0.00 3.06
113 114 4.761227 GGTAATTTTCTACAAACCCGGTCA 59.239 41.667 0.00 0.00 0.00 4.02
114 115 4.142838 CGGTAATTTTCTACAAACCCGGTC 60.143 45.833 0.00 0.00 0.00 4.79
115 116 3.752747 CGGTAATTTTCTACAAACCCGGT 59.247 43.478 0.00 0.00 0.00 5.28
116 117 3.426560 GCGGTAATTTTCTACAAACCCGG 60.427 47.826 0.00 0.00 33.74 5.73
117 118 3.188873 TGCGGTAATTTTCTACAAACCCG 59.811 43.478 0.00 0.00 36.11 5.28
118 119 4.769859 TGCGGTAATTTTCTACAAACCC 57.230 40.909 0.00 0.00 0.00 4.11
119 120 5.400188 GTGTTGCGGTAATTTTCTACAAACC 59.600 40.000 0.00 0.00 0.00 3.27
120 121 5.972382 TGTGTTGCGGTAATTTTCTACAAAC 59.028 36.000 0.00 0.00 0.00 2.93
121 122 6.132791 TGTGTTGCGGTAATTTTCTACAAA 57.867 33.333 0.00 0.00 0.00 2.83
122 123 5.752892 TGTGTTGCGGTAATTTTCTACAA 57.247 34.783 0.00 0.00 0.00 2.41
123 124 5.505985 GGTTGTGTTGCGGTAATTTTCTACA 60.506 40.000 0.00 0.00 0.00 2.74
124 125 4.913345 GGTTGTGTTGCGGTAATTTTCTAC 59.087 41.667 0.00 0.00 0.00 2.59
125 126 4.822896 AGGTTGTGTTGCGGTAATTTTCTA 59.177 37.500 0.00 0.00 0.00 2.10
126 127 3.634910 AGGTTGTGTTGCGGTAATTTTCT 59.365 39.130 0.00 0.00 0.00 2.52
127 128 3.972403 AGGTTGTGTTGCGGTAATTTTC 58.028 40.909 0.00 0.00 0.00 2.29
128 129 4.394439 AAGGTTGTGTTGCGGTAATTTT 57.606 36.364 0.00 0.00 0.00 1.82
129 130 4.116238 CAAAGGTTGTGTTGCGGTAATTT 58.884 39.130 0.00 0.00 0.00 1.82
130 131 3.131400 ACAAAGGTTGTGTTGCGGTAATT 59.869 39.130 0.00 0.00 43.48 1.40
131 132 2.691011 ACAAAGGTTGTGTTGCGGTAAT 59.309 40.909 0.00 0.00 43.48 1.89
132 133 2.093106 ACAAAGGTTGTGTTGCGGTAA 58.907 42.857 0.00 0.00 43.48 2.85
133 134 1.752683 ACAAAGGTTGTGTTGCGGTA 58.247 45.000 0.00 0.00 43.48 4.02
134 135 0.892063 AACAAAGGTTGTGTTGCGGT 59.108 45.000 0.00 0.00 44.59 5.68
135 136 1.276415 CAACAAAGGTTGTGTTGCGG 58.724 50.000 4.52 0.00 46.63 5.69
144 145 6.418057 TCCTTTATCATTGCAACAAAGGTT 57.582 33.333 26.65 2.94 43.68 3.50
145 146 6.211184 TCATCCTTTATCATTGCAACAAAGGT 59.789 34.615 26.65 18.21 43.68 3.50
146 147 6.532657 GTCATCCTTTATCATTGCAACAAAGG 59.467 38.462 24.34 24.34 44.31 3.11
147 148 6.252015 CGTCATCCTTTATCATTGCAACAAAG 59.748 38.462 0.00 9.19 0.00 2.77
148 149 6.092092 CGTCATCCTTTATCATTGCAACAAA 58.908 36.000 0.00 0.00 0.00 2.83
149 150 5.639757 CGTCATCCTTTATCATTGCAACAA 58.360 37.500 0.00 0.00 0.00 2.83
150 151 4.438608 GCGTCATCCTTTATCATTGCAACA 60.439 41.667 0.00 0.00 0.00 3.33
151 152 4.037690 GCGTCATCCTTTATCATTGCAAC 58.962 43.478 0.00 0.00 0.00 4.17
152 153 3.947196 AGCGTCATCCTTTATCATTGCAA 59.053 39.130 0.00 0.00 0.00 4.08
153 154 3.544684 AGCGTCATCCTTTATCATTGCA 58.455 40.909 0.00 0.00 0.00 4.08
154 155 4.558538 AAGCGTCATCCTTTATCATTGC 57.441 40.909 0.00 0.00 0.00 3.56
155 156 6.138761 GCTTAAGCGTCATCCTTTATCATTG 58.861 40.000 12.53 0.00 0.00 2.82
156 157 6.305693 GCTTAAGCGTCATCCTTTATCATT 57.694 37.500 12.53 0.00 0.00 2.57
157 158 5.931441 GCTTAAGCGTCATCCTTTATCAT 57.069 39.130 12.53 0.00 0.00 2.45
172 173 2.302478 GCTAGGTGAGCGCTTAAGC 58.698 57.895 17.83 17.83 42.62 3.09
181 182 0.671251 GTCGGATCTGGCTAGGTGAG 59.329 60.000 0.00 0.00 0.00 3.51
182 183 1.101635 CGTCGGATCTGGCTAGGTGA 61.102 60.000 4.31 0.00 0.00 4.02
183 184 1.360551 CGTCGGATCTGGCTAGGTG 59.639 63.158 4.31 0.00 0.00 4.00
184 185 0.683504 AACGTCGGATCTGGCTAGGT 60.684 55.000 4.31 0.00 0.00 3.08
185 186 0.460311 AAACGTCGGATCTGGCTAGG 59.540 55.000 4.31 0.00 0.00 3.02
186 187 1.841450 GAAACGTCGGATCTGGCTAG 58.159 55.000 4.31 0.00 0.00 3.42
187 188 0.099968 CGAAACGTCGGATCTGGCTA 59.900 55.000 4.31 0.00 43.81 3.93
188 189 1.153823 CGAAACGTCGGATCTGGCT 60.154 57.895 4.31 0.00 43.81 4.75
189 190 3.384927 CGAAACGTCGGATCTGGC 58.615 61.111 0.62 0.00 43.81 4.85
198 199 1.079875 TTATGGCCTCGCGAAACGTC 61.080 55.000 11.33 2.34 44.19 4.34
199 200 0.671163 TTTATGGCCTCGCGAAACGT 60.671 50.000 11.33 7.28 44.19 3.99
200 201 0.655733 ATTTATGGCCTCGCGAAACG 59.344 50.000 11.33 1.17 45.62 3.60
201 202 1.668751 TCATTTATGGCCTCGCGAAAC 59.331 47.619 11.33 4.66 0.00 2.78
202 203 2.031258 TCATTTATGGCCTCGCGAAA 57.969 45.000 11.33 0.00 0.00 3.46
203 204 2.031258 TTCATTTATGGCCTCGCGAA 57.969 45.000 11.33 0.00 0.00 4.70
204 205 2.254546 ATTCATTTATGGCCTCGCGA 57.745 45.000 9.26 9.26 0.00 5.87
205 206 3.745975 TCTAATTCATTTATGGCCTCGCG 59.254 43.478 3.32 0.00 0.00 5.87
206 207 4.757149 ACTCTAATTCATTTATGGCCTCGC 59.243 41.667 3.32 0.00 0.00 5.03
207 208 7.819415 TCATACTCTAATTCATTTATGGCCTCG 59.181 37.037 3.32 0.00 0.00 4.63
208 209 9.507329 TTCATACTCTAATTCATTTATGGCCTC 57.493 33.333 3.32 0.00 0.00 4.70
209 210 9.289782 GTTCATACTCTAATTCATTTATGGCCT 57.710 33.333 3.32 0.00 0.00 5.19
210 211 9.289782 AGTTCATACTCTAATTCATTTATGGCC 57.710 33.333 0.00 0.00 0.00 5.36
230 231 4.352009 TGGCATGTAAATCCCAAGTTCAT 58.648 39.130 0.00 0.00 0.00 2.57
251 252 6.037786 TGTTAAGGGAGTGATGTTCTACTG 57.962 41.667 0.00 0.00 0.00 2.74
293 294 7.562454 ACTCTGTTATGAAGTTTCGGAAAAA 57.438 32.000 4.46 0.00 0.00 1.94
299 300 8.070171 ACATGAAAACTCTGTTATGAAGTTTCG 58.930 33.333 0.00 0.00 32.39 3.46
309 310 7.397892 TGAAAACCACATGAAAACTCTGTTA 57.602 32.000 0.00 0.00 0.00 2.41
324 325 2.222729 CGGTCGAATCGATGAAAACCAC 60.223 50.000 9.10 0.00 38.42 4.16
325 326 1.996898 CGGTCGAATCGATGAAAACCA 59.003 47.619 9.10 0.00 38.42 3.67
331 332 0.104120 ATTGCCGGTCGAATCGATGA 59.896 50.000 9.10 0.00 38.42 2.92
332 333 0.233074 CATTGCCGGTCGAATCGATG 59.767 55.000 9.10 4.72 38.42 3.84
343 392 1.444895 GCTTTGCTGTCATTGCCGG 60.445 57.895 0.00 0.00 0.00 6.13
368 417 1.676529 GAGTGTCATCGCTAGTGCCTA 59.323 52.381 0.00 0.00 34.29 3.93
369 418 0.457851 GAGTGTCATCGCTAGTGCCT 59.542 55.000 0.00 0.00 34.29 4.75
370 419 0.867753 CGAGTGTCATCGCTAGTGCC 60.868 60.000 0.00 0.00 35.66 5.01
371 420 2.571528 CGAGTGTCATCGCTAGTGC 58.428 57.895 0.00 0.00 35.66 4.40
553 640 2.852495 CTTACCCAGCATGACGGCGT 62.852 60.000 14.65 14.65 39.69 5.68
569 656 1.418334 GAGCCTCTCCTCCATGCTTA 58.582 55.000 0.00 0.00 31.23 3.09
735 4044 2.252714 GGTCTTCACTCTGTTCCTCCT 58.747 52.381 0.00 0.00 0.00 3.69
1332 4676 4.137872 TCGCCGGCGTTTAGGAGG 62.138 66.667 44.16 17.22 40.74 4.30
1854 5285 1.227263 CGAACCGAATCTCCCGCAT 60.227 57.895 0.00 0.00 0.00 4.73
2431 5913 6.901265 TCAAGGTTAAGCGTAAAATGTTACC 58.099 36.000 0.00 0.00 36.96 2.85
2444 5926 5.036117 TCCAGTCCATATCAAGGTTAAGC 57.964 43.478 0.00 0.00 0.00 3.09
2447 5929 6.012858 ACACTTTCCAGTCCATATCAAGGTTA 60.013 38.462 0.00 0.00 0.00 2.85
2734 6239 3.744426 GCTCATGCACAAAAGCTGAAAAT 59.256 39.130 0.00 0.00 39.41 1.82
2742 6247 6.187125 AGTAATACAGCTCATGCACAAAAG 57.813 37.500 0.00 0.00 42.74 2.27
2841 6357 1.901591 ATTGAAGACCACCAGTGCAG 58.098 50.000 0.00 0.00 0.00 4.41
2915 6432 5.038033 CCGCTAAAGACAGACTTCAGATAC 58.962 45.833 0.00 0.00 37.93 2.24
2936 6481 2.156504 GCACGATCAGATTAGCATTCCG 59.843 50.000 0.00 0.00 0.00 4.30
3502 11193 2.158385 AGAGGTGAACTGTCAGGACTCT 60.158 50.000 4.53 6.52 36.48 3.24
3607 11312 1.871080 AGAAACACAAGAGCTGACGG 58.129 50.000 0.00 0.00 0.00 4.79
3609 11314 3.303659 GCAGAAGAAACACAAGAGCTGAC 60.304 47.826 0.00 0.00 0.00 3.51
3697 11402 2.571653 AGGAAGCAGTAGCAACCACATA 59.428 45.455 0.00 0.00 45.49 2.29
3905 11695 5.448926 AAACAAGATCAAAACGTTGCAAC 57.551 34.783 19.89 19.89 34.50 4.17
4122 11934 1.063417 CCTTTCCTGATCCTTGGCCAT 60.063 52.381 6.09 0.00 0.00 4.40
4271 12083 1.347707 CTGAGGCAGTTACCAGTTGGA 59.652 52.381 4.92 0.00 38.94 3.53
4306 12131 2.364160 GGCACCCCCATTGGATGT 59.636 61.111 3.62 0.00 35.39 3.06
4421 12247 3.891366 ACCCTTCATTGGACTGAAACTTG 59.109 43.478 0.00 0.00 34.86 3.16


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.